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Helena
@hexylena:matrix.org
[m]
😬
bgruening
@bgruening:matrix.org
[m]
pvanheusden: M Bernt said the tools are "ok" but using Docker. So we can install them on EU if you like, I'm happy to take PRs into a seperate qiime2.yml file
M Bernt
@bernt-matthias:matrix.org
[m]
Qiime2 requires 22.05 only because of the new/updated datatypes for qza/qzv ..
Tools seem to work (I use the docker image with singularity) .. only the import tool is a bit "clumsy":
  • provides a ton of options .. but users typically will only need 2 regarding fastq import
  • fastq files need to be in a collection (even if paired) .. names of the collection elements are important
1 reply
Saskia Hiltemann
@shiltemann:matrix.org
[m]

Hi All!

It's just about that time again to start organising the next Smorgasbord event. This year we would love some additional help in the organisation of the event. We will discuss it in tomorrow's GOATs meeting (15:00 CET, 09:00 EST), so please join the meeting if you are interested in possibly helping out! (anybody is welcome!)

Here is the agenda for this Smorgasbord discussion if you want a sneak peek; we will discuss different ways to help out, hopefully pick/narrow down a date, etc.

For anybody who cannot make it tomorrow but would like to help out with organisation, let me know (send me a message, or just add your name to the agenda under "apologies") and we will organize a second call (probably needed for timezone reasons already anyway)

For anybody else who is just excited to participate in this event: We hope to announce the dates in the coming weeks, so keep your eyes on this channel and the GTN Slack for news

Cheers!

bgruening
@bgruening:matrix.org
[m]
yes, it can :)
M Bernt
@bernt-matthias:matrix.org
[m]
pvanheusden: works like a charm with singularity (never had problems with running docker containers with singularity)
If you want to use the tools on a Galaxy <22.05 then you might
M Bernt
@bernt-matthias:matrix.org
[m]
Was just searching for a videos we mad for this https://gallantries.github.io/video-library/videos/dev/tool-from-scratch/tutorial/ and noticed that the 2021 listing includes only one of the videos ..
Helena
@hexylena:matrix.org
[m]
that's a special case, one time it was filmed as 5 separate parts, and once as a single logical unit.
or maybe we just dropped something accidentally. I'll check.
M Bernt
@bernt-matthias:matrix.org
[m]

Thanks .. I found the video I was looking for any way.. so I'm fine

Was just wondering if this was intended

Helena
@hexylena:matrix.org
[m]
what's the video ID?
not intended, no, we want to have every version of every video
GTN Bot
@gtn-bot:matrix.org
[m]

GTN News for Nov 23

Big News!

Wendi Bacon
@nomadscientist:matrix.org
[m]
Does anyone have an example history calculating a Chi Square within Galaxy?
utpalh
@utpalh
how do i integrate apollo with galaxy. i install galaxy with ansible.
2 replies
Helena
@hexylena:matrix.org
[m]
there are not, the topic of deploying galaxy + apollo connected together is really an advanced admin deployment setup.
Is your end goal setting up a galaxy+apollo for a local lab? Just using it for yourself for annotation? Or something different?
https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment we built this at one point specifically for the case of making it easier to deploy these things, but it's a bit out of date, unfortunately.
utpalh
@utpalh
This is for my lab. because the cpt and some galaxy are not available with good connection in my country
Helena
@hexylena:matrix.org
[m]
Fair enough!
utpalh
@utpalh
Is there a way you can help me to configure it
Helena
@hexylena:matrix.org
[m]
I'm really sorry about the complete lack of documentation here, it's such a rarely used deployment unfortunately that so far not many people other than Anthony Bretaudeau and I have deployed it.
We'd love to update the dockerized-gmod-deployment, but without an updated Galaxy image it feels like a waste. But myabe we can share with you how to re-use the rest as docker containers, to save some time.
utpalh
@utpalh
I also found that some of the tools used by CPT are inhouse and not available in the toolshed for the phage annotation pipeline.
Helena
@hexylena:matrix.org
[m]
yeah, they're actively working on that. It takes some time though.
Let's move this conversation over to https://gitter.im/galaxy-genome-annotation/Lobby where it's all galaxy+genome annotation people (including CPT staff!)
pvanheusden
@pvanheusden:matrix.org
[m]
Hey everyone... I have to do a demo and sadly my server crashed. I noticed JupyTool on .eu - can I use this to make a runnable notebook? i.e. if I feed it a notebook and an input can I use it in a workflow?
2nd question - by accident I spawned many interactive tools - can I select them all somehow and shut them down?
bgruening
@bgruening:matrix.org
[m]
yes you can use it
yes you can use it in workflows
Let me know if I can help in any way.
pvanheusden
@pvanheusden:matrix.org
[m]
thanks but the problem is how many are running...
and there doesn't seems to be a choose all...
bgruening
@bgruening:matrix.org
[m]
I will take care
done
Comrade MechAtürk 🇹🇷 ☭
@InfraKemal_twitter
Hi Guys! I am a year 12 student and I have to write an individual assessment in Biology. I want to analyze the changes in amino acids in the genes BRCA1 and BRCA2. To do this I want to use snpEff eff in a galaxy server. When I input the VCF file for the human genome and use a .bed file with the intervals of the BRCA1 and 2 genes and execute, the following error is displayed: "Unrecognized genomig interval file type". I would be very thankful if anyone could help me here! Thanks in advance!!
3 replies
GTN Bot
@gtn-bot:matrix.org
[m]

GTN News for Nov 25

Big News!

Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
That way https://youtu.be/\_uQrN45zkmE @InfraKemal_twitter
2 replies
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Thanks, let me check
3 replies
maaryaam-gh
@maaryaam-gh
Hello, how can I find out the highest and lowest expression values in a large matrix of single cell gene expression data whose number of columns and rows is greater than 1000?
pvanheusden
@pvanheusden:matrix.org
[m]
hey there... I have some viral contigs assembled with Shovill/Spades - does anyone know a tool that I can use to orient them using a related reference? right now I can map them to the reference with minimap2 but I'd like to use the resulting orientation to "stitch" them together into a final contig (well, scaffold).
Anton Nekrutenko
@nekruten:matrix.org
[m]
There must be something within unicycle et for that bu to in may be wrong
pvanheusden
@pvanheusden:matrix.org
[m]
hm, I hadn't thought of unicycler for that, but let me try
pvanheusden
@pvanheusden:matrix.org
[m]
but I don't think that that is designed for scaffolding. some people seem to use the output of nucmer... there's a fair amount of code in Broad's toolkit: https://github.com/broadinstitute/viral-assemble/blob/master/assembly.py
Helena
@hexylena:matrix.org
[m]

We have some sad news to share, Simon Gladman (@slugger70) has passed away over the weekend. He was such an integral part of the Galaxy Training community, especially admin training, sharing all of his knowledge from years of building, running, and scaling UseGalaxy.org.au. Additionally he was a fantastic bioinformatics teacher, and wrote a lot of the assembly tutorials in the GTN. He had deep knowledge about the subject and was fantastic at communicating that clearly and with a touch of typical Simon humour. I'd always hoped to get to teach alongside him on those topics someday.

His colleagues have posted this in memoriam, and if you want to share any memories of him: https://www.biocommons.org.au/news/simon-gladman